ScanITD
Introduction
ScanITD: detecting internal tandem duplication with robust variant allele frequency estimation
Getting Started
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.
Prerequisites
You need Python 3.4 and later to run ScanITD.
install necessary python packages via anaconda
Install anaconda (python 3.7) firstly, then install dependent packages via conda in bioconda channel.
conda install -c bioconda pysam
conda install -c conda-forge scikit-bio
conda install -c anaconda numpy
conda install -c bioconda samtools ## samtools/1.0 or newer is required
Usage
ScanITD.py -i input_bam_file -r indexed_refenence_genome_fasta -o output_vcf_filename_prefix [opts]
Options:
-h, --help show this help message and exit
-i INPUT, --input INPUT
BWA-MEM BAM file
-r REF, --ref REF reference genome in FASTA format
-o OUTPUT, --output OUTPUT
output prefix
-m MAPQ, --mapq MAPQ minimal MAPQ in BAM for calling ITD (default: 15)
-c AO, --ao AO minimal observation count for ITD (default: 4)
-d DP, --depth DP minimal depth to call ITD (default: 10)
-f VAF, --vaf VAF minimal variant allele frequency (default: 0.1)
-l ITD_LEN, --len ITD_LEN
minimal ITD length to report (default: 10)
-n MISMATCH maximum allowed mismatch bases of pairwise local
alignment (default: 3)
-t TARGET, --target TARGET
Limit analysis to targets listed in the BED-format
file or a samtools region string
-k, --keep Kepp the ITD build BAM file
-v, --version show program's version number and exit
Input:
input_bam_file :input WES BAM file. (e.g., wes-seq.bam)
indexed_reference_genome_fasta :specify reference genome in FASTA format (the reference genome should be indexed)
Output:
output_vcf_filename_prefix :specify the prefix of the output vcf file
The name of the output VCF file will be prefix.itd.vcf.
The Test directory contains files and scripts for testing the installation.
License
This project is licensed under MIT.
Contact
Bug reports or feature requests can be submitted on the ScanITD Github page.
Citation
Wang TY. and Yang R. ScanITD: Detecting internal tandem duplication with robust variant allele frequency estimation.